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If earl is so smart wouldn't he know the name of a foreign country?
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Marcus did not add a file to the folder of Flying Rhino. He forgot.
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Earl says that he couldn't particapate in atheletic events because of "an inner ear problem" namely that he kept hearing voices, we then see that the voices are telling him about how innept he is at sports. This suggests that his real problem was scitsofrenia.
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When Ruby got stuck, she was yelling Lydia that she's there, but on closed captioning, the first letter of her name was capitals, and the rest of her name was at low caps before the rest of the sentence was capitals.
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Earl's eyes keep changing colours.
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When Mr. Needlenose says he will put his foot down to the Ruby clones' order to put more lines in the play, Fred Smertz says Mr. Needlenose is fired. How can a student in junior high fire a staff member? He doesn't even work for them!
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Coincidentally, in the closed captioning for the title sequence, it says "the phantom face is funny"
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The words on the side of the milk carton say, "have you seen this genius?" with a picture of Earl.
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We learn that Billy is allergic to sand.